Sequence-specific assignments and their use in NMR studies of DNA structure

1987 ◽  
Vol 20 (1-2) ◽  
pp. 1-34 ◽  
Author(s):  
B. R. Reid
Keyword(s):  
Dna Sequences ◽  
Nearest Neighbor ◽  
Context Effects ◽  
Double Helix ◽  
Dna Structure ◽  
Nmr Studies ◽  
Specific Sequence ◽  
X Ray ◽  
Fibre Diffraction ◽  
Number Of Publications

There has been a surge of recent interest, reflected by a sharp increase in the number of publications, in the area of high-resolution nuclear magnetic resonance (NMR) studies of DNA. The goal of many of these studies is to monitor the structure of biologically important DNA sequences directly in solution; the impetus for such studies was the realization, from early single-crystal X-ray structures, that nearest-neighbor context effects are a major determinant of local structure in short double-helical DNAs (Dickerson & Drew, 1981; Dickerson, 1983). Thus, instead of the previously assumed regular averaged structure of the double helix derived from fibre diffraction analysis, the more interesting concept emerged that specific sequence-dependent distortions from ‘classical’ DNA structure might be responsible for the recognition of such sequences by a variety of ligands such as repressors, polymerases, drugs, etc.

scholarly journals Water–DNA interactions as studied by X–ray and neutron fibre diffraction

2004 ◽  
Vol 359 (1448) ◽  
pp. 1237-1248 ◽  
Author(s):  
Watson Fuller ◽  
Trevor Forsyth ◽  
Arumugam Mahendrasingam
Keyword(s):  
Structural Information ◽  
Double Helix ◽  
Water Environment ◽  
Structural Features ◽  
Molecular Conformations ◽  
X Ray ◽  
Biochemical Processes ◽  
Fibre Diffraction ◽  
Dna Double Helix ◽  
High Degree

X–ray fibre–diffraction studies indicate a high degree of stereochemical specificity in interactions between water and the DNA double helix. Evidence for this comes from data that show that the molecular conformations assumed by DNA in fibres are highly reproducible and that the hydration–driven transitions between these conformations are fully reversible. These conformational transitions are induced by varying the relative humidity of the fibre environment and hence its water content. Further evidence for stereochemical specificity comes from the observed dependence of the conformation assumed on the ionic content of the fibre and the nucleotide sequence of the DNA. For some transitions, information on stereochemical pathways has come from real–time X–ray fibre diffraction using synchrotron radiation; information on the location of water with respect to the double helix for a number of DNA conformations has come from neutron fibre diffraction. This structural information from fibre–diffraction studies of DNA is complemented by information from X–ray single–crystal studies of oligonucleotides. If the biochemical processes involving DNA have evolved to exploit the structural features observed in DNA fibres and oligonucleotide single crystals, the challenges in developing alternatives to a water environment can be expected to be very severe.

scholarly journals Exploring DNA structures in real-time polymerase kinetics using Pacific Biosciences sequencer data

2013 ◽  
Author(s):  
Sterling Sawaya ◽  
James Boocock ◽  
Mik Black ◽  
Neil Gemmell
Keyword(s):  
Real Time ◽  
Dna Sequences ◽  
Double Helix ◽  
Dna Structure ◽  
R Package ◽  
Dna Structures ◽  
Pacific Biosciences ◽  
Tandem Repeat Sequences ◽  
The Pacific ◽  
Polymerase Pausing

Pausing of DNA polymerase can indicate the presence of a DNA structure that differs from the canonical double-helix. Here we detail a method to investigate how polymerase pausing in the Pacific Biosciences sequencer reads can be related to DNA structure. The Pacific Biosciences sequencer uses optics to view a polymerase and its interaction with a single DNA molecule in real-time, offering a unique way to detect potential alternative DNA structures. We have developed a new way to examine polymerase kinetics and relate it to the DNA sequence by using a wavelet transform of read information from the sequencer. We use this method to examine how polymerase kinetics are related to nucleotide base composition. We then examine tandem repeat sequences known for their ability to form different DNA structures: (CGG)n and (CG)n repeats which can, respectively, form G-quadruplex DNA and Z-DNA. We find pausing around the (CGG)n repeat that may indicate the presence of G-quadruplexes in some of the sequencer reads. The (CG)n repeat does not appear to cause polymerase pausing, but its kinetics signature nevertheless suggests the possibility that alternative nucleotide conformations may sometimes be present. We discuss the implications of using our method to discover DNA sequences capable of forming alternative structures. The analyses presented here can be reproduced on any Pacific Biosciences kinetics data for any DNA pattern of interest using an R package that we have made publicly available.

Comparison of the Global Genomic and Transcription-Coupled Repair Rates of Different Lesions in Human Cells

2004 ◽  
Vol 59 (5-6) ◽  
pp. 445-453 ◽  
Author(s):  
Boyko Atanassov ◽  
Aneliya Velkova ◽  
Emil Mladenov ◽  
Boyka Anachkova ◽  
George Russev
Keyword(s):  
Dna Sequences ◽  
Chemical Nature ◽  
Excision Repair ◽  
Uv Light ◽  
Double Helix ◽  
Human Cells ◽  
The Other ◽  
Specific Sequence ◽  
Dna Double Helix ◽  
Transcription Coupled Repair

There are two subclasses of nucleotide excision repair (NER). One is the global genomic repair (GGR) which removes lesions throughout the genome regardless of whether any specific sequence is transcribed or not. The other is the transcription-coupled repair (TCR), which removes lesions only from the transcribed DNA sequences. There are data that GGR rates depend on the chemical nature of the lesions in a manner that the lesions inflicting larger distortion on the DNA double helix are repaired at higher rate. It is not known whether the TCR repair rates depend on the type of lesions and in what way. To address this question human cells were transfected with pEGFP and pEYFP plasmids treated with UV light, cis-diamminedichloroplatinum(II) (cisplatin) and angelicin and 24 h later the restored fluorescence was measured and used to calculate the respective NER rates. In a parallel series of experiments the same plasmids were incubated in repair-competent protein extracts to determine GGR rates in the absence of transcription. From the two sets of data, the TCR rates were calculated. We found out that cisplatin, UV light and angelicin lesions were repaired by GGR with different efficiency, which corresponded to the degree of DNA helix distortion induced by these agents. On the other hand the three lesions were repaired by TCR at very similar rates which showed that TCR efficiency was not directly connected with the chemical nature of the lesions.

scholarly journals Maurice Hugh Frederick Wilkins. 15 December 1916 — 5 October 2004

2006 ◽  
Vol 52 ◽  
pp. 455-478
Author(s):  
Struther Arnott ◽  
T.W.B. Kibble ◽  
Tim Shallice
Keyword(s):  
Secondary Structure ◽  
Nucleic Acids ◽  
Double Helix ◽  
Genetic Material ◽  
Research Programme ◽  
Dna Structure ◽  
X Ray Diffraction ◽  
Symmetrical Structure ◽  
X Ray ◽  
The Third

Maurice Hugh Frederick Wilkins was the ‘Third man of the double helix’ according to the publishers who were allowed to foist this title on his late–written autobiography. Certainly it is for his role in the discovery of the duplex secondary structure of DNA that he will be remembered. It might be argued that he was the first man, rather than the third, for it was his successful revival of X–ray diffraction studies of DNA and their earliest product in 1950, a pattern of a well–oriented and polycrystalline DNA of unprecedented quality, that allowed him to conclude almost immediately that the basic framework of the genetic material was simple and symmetrical, and that the symmetrical structure took the form of a helix. This same pattern, displayed at a conference in Naples six months later, was the major inspiration for the involvement of J. D. Watson (ForMemRS 1981) in modelling DNA structure in collaboration with F. H. C. Crick (FRS 1959). Crick was a personal friend of Maurice's and was more involved with studies of proteins until the progress of Maurice's research programme and Watson's enthusiastic presence in Cambridge convinced him to put nucleic acids first. The carefully crafted citation for the 1960 Lasker Award, which these three men shared in 1960, put Maurice's name first and accurately referred to ‘… the painstaking x–ray diffraction studies of Wilkins that provided a most important clue that was pursued in an ingenious fashion and to a logical conclusion by Crick and Watson…’. Maurice's diffraction studies of DNA were not only the alpha but also the omega of the double helix because it was left to him to remedy a major flaw in the original (1953) Watson–Crick conjecture.

New Copper Compounds with Antiplatelet Aggregation Activity

2019 ◽  
Vol 15 (8) ◽  
pp. 850-862
Author(s):  
Mirthala Flores-García ◽  
Juan Manuel Fernández-G. ◽  
Cristina Busqueta-Griera ◽  
Elizabeth Gómez ◽  
Simón Hernández-Ortega ◽  
...  
Keyword(s):  
Schiff Base ◽  
Solid State ◽  
Thrombotic Event ◽  
X Ray Diffraction ◽  
Nmr Studies ◽  
Schiff Base Ligands ◽  
X Ray ◽  
Antiplatelet Aggregation ◽  
Aggregation Activity ◽  
L1 And L2

Background: Ischemic heart disease, cerebrovascular accident, and venous thromboembolism have the presence of a thrombotic event in common and represent the most common causes of death within the population. Objective: Since Schiff base copper(II) complexes are able to interact with polyphosphates (PolyP), a procoagulant and potentially prothrombotic platelet agent, we investigated the antiplatelet aggregating properties of two novel tridentate Schiff base ligands and their corresponding copper( II) complexes. Methods: The Schiff base ligands (L1) and (L2), as well as their corresponding copper(II) complexes (C1) and (C2), were synthesized and characterized by chemical analysis, X-ray diffraction, mass spectrometry, and UV-Visible, IR and far IR spectroscopy. In addition, EPR studies were carried out for (C1) and (C2), while (L1) and (L2) were further analyzed by 1H and 13C NMR. Tests for antiplatelet aggregation activities of all of the four compounds were conducted. Results: X-ray diffraction studies show that (L1) and (L2) exist in the enol-imine tautomeric form with a strong intramolecular hydrogen bond. NMR studies show that both ligands are found as enol-imine tautomers in CDCl3 solution. In the solid state, the geometry around the copper(II) ion in both (C1) and (C2) is square planar. EPR spectra suggest that the geometry of the complexes is similar to that observed in the solid state by X-ray crystallography. Compound (C2) exhibited the strongest antiplatelet aggregation activity. Conclusion: Schiff base copper(II) complexes, which are attracting increasing interest, could represent a new approach to treat thrombosis by blocking the activity of PolyP with a potential anticoagulant activity and, most importantly, demonstrating no adverse bleeding events.

Solution multinuclear (31P,111Cd,77Se) magnetic resonance studies of cadmium complexes of heterocyclic aromatic thiones and the structure of [tetrakis(2(1H)-pyridinethione)cadmium] nitrate, [Cd(C5H5NS)4](NO3)2

2000 ◽  
Vol 78 (5) ◽  
pp. 590-597 ◽  
Author(s):  
Umarani Rajalingam ◽  
Philip AW Dean ◽  
Hilary A Jenkins
Keyword(s):  
Cadmium Nitrate ◽  
Cadmium Complexes ◽  
Nmr Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Stoichiometric Reaction ◽  
Complex Salts ◽  
Reduced Temperature ◽  
Aromatic Heterocyclic ◽  
Phosphine Chalcogenides

The complex salts CdL4(O3SCF3)2 (L = 2(1H)-pyridinethione (Py2SH), 4(1H)-pyridinethione (Py4SH), or 2(1H)-quinolinethione (Q2SH)) have been synthesized by the stoichiometric reaction of Cd(O3SCF3)2 and the appropriate thione. Both ambient-temperature 13C and reduced-temperature 111Cd NMR of CdL4(O3SCF3)2 in solution are consistent with L being bound through sulfur. Reduced-temperature NMR (31P, 77Se, 111Cd, as appropriate) of mixtures of CdL4(O3SCF3)2 and Cd(EPCy3)4(O3SCF3)2 (E = Se, Cy = c-C6H11) and of Cd(EPCy3)4(O3SCF3)2 (E = S, Se) and L in solution provides evidence for various [CdLn(EPCy3)4-n]2+. Similarly, reduced-temperature metal NMR of [CdL4]2+ and [CdL'4]2+ (L, L' = Py2SH, Py4SH, Q2SH; L not equal L') in solution shows the formation of [CdLnL'4-n]2+. Thus it has been demonstrated that at reduced temperature [CdL4]2+ is intact in solution and exchange of L is slow on the timescale of the metal chemical shift differences. From the NMR studies of Cd(EPCy3)4(O3SCF3)2 (E = S, Se):L mixtures, the binding preferences are found to be L > EPCy3 in solution. Similarly, from the reduced temperature metal NMR spectra of mixtures where L and L' compete for Cd(II) in solution, the binding preferences are Py4SH > Py2SH > Q2SH. The structure of Cd(Py2SH)4(NO3)2 (4) has been determined by single crystal X-ray analysis. Colorless crystals of 4 are tetragonal, I4(1)/acd with 8 molecules per unit cell of dimensions a = 18.660(3), c = 15.215(3) Å. The structure is comprised of recognizable NO3- anions and [Cd(Py2SH)4]2+ cations. In the cations, which have S4 symmetry, the ligands are S-bound. A network of NH···O hydrogen bonds links the cations and anions.Key words: aromatic heterocyclic thiones, cadmium complexes, phosphine chalcogenides, 111Cd, 31P, 77Se NMR, X-ray crystallography.

scholarly journals Comprehensive Characterisation of the Ketoprofen-β-Cyclodextrin Inclusion Complex Using X-ray Techniques and NMR Spectroscopy

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 4089
Author(s):  
Katarzyna Betlejewska-Kielak ◽  
Elżbieta Bednarek ◽  
Armand Budzianowski ◽  
Katarzyna Michalska ◽  
Jan K. Maurin
Keyword(s):  
Nmr Spectroscopy ◽  
Inclusion Complex ◽  
Crystal And Molecular Structure ◽  
Binding Constants ◽  
Nmr Studies ◽  
X Ray ◽  
Cyclodextrin Inclusion ◽  
Powder Samples ◽  
Cyclodextrin Inclusion Complex ◽  
Co Precipitation

Racemic ketoprofen (KP) and β-cyclodextrin (β-CD) powder samples from co-precipitation (1), evaporation (2), and heating-under-reflux (3) were analysed using X-ray techniques and nuclear magnetic resonance (NMR) spectroscopy. On the basis of NMR studies carried out in an aqueous solution, it was found that in the samples obtained by methods 1 and 2, there were large excesses of β-CD in relation to KP, 10 and 75 times, respectively, while the sample obtained by method 3 contained equimolar amounts of β-CD and KP. NMR results indicated that KP/β-CD inclusion complexes were formed and the estimated binding constants were approximately 2400 M−1, showing that KP is quite strongly associated with β-CD. On the other hand, the X-ray single-crystal technique in the solid state revealed that the (S)-KP/β-CD inclusion complex with a stoichiometry of 2:2 was obtained as a result of heating-under-reflux, for which the crystal and molecular structure were examined. Among the methods used for the preparation of the KP/β-CD complex, only method 3 is suitable.

scholarly journals Combination of Dual-Energy X-ray Transmission and Variable Gas-Ejection for the In-Line Automatic Sorting of Many Types of Scrap in One Measurement

2021 ◽  
Vol 11 (10) ◽  
pp. 4349
Author(s):  
Tianzhong Xiong ◽  
Wenhua Ye ◽  
Xiang Xu
Keyword(s):  
High Efficiency ◽  
Nearest Neighbor ◽  
High Energy ◽  
Dual Energy ◽  
Center Of Gravity ◽  
Low Energy ◽  
Identification Accuracy ◽  
Flow Process ◽  
X Ray ◽  
Automatic Sorting

As an important part of pretreatment before recycling, sorting has a great impact on the quality, efficiency, cost and difficulty of recycling. In this paper, dual-energy X-ray transmission (DE-XRT) combined with variable gas-ejection is used to improve the quality and efficiency of in-line automatic sorting of waste non-ferrous metals. A method was proposed to judge the sorting ability, identify the types, and calculate the mass and center-of-gravity coordinates according to the shading of low-energy, the line scan direction coordinate and transparency natural logarithm ratio of low energy to high energy (R_value). The material identification was satisfied by the nearest neighbor algorithm of effective points in the material range to the R_value calibration surface. The flow-process of identification was also presented. Based on the thickness of the calibration surface, the material mass and center-of-gravity coordinates were calculated. The feasibility of controlling material falling points by variable gas-ejection was analyzed. The experimental verification of self-made materials showed that identification accuracy by count basis was 85%, mass and center-of-gravity coordinates calculation errors were both below 5%. The method proposed features high accuracy, high efficiency, and low operation cost and is of great application value even to other solid waste sorting, such as plastics, glass and ceramics.

ChemInform Abstract: M2Ga6Te10 (M: Li, Na): Two New Non-Metallic Filled β-Manganese Phases - X-Ray and NMR Studies.

ChemInform ◽  
2010 ◽  
Vol 31 (15) ◽  
pp. no-no
Author(s):  
H. J. Deiseroth ◽  
L. Kienle ◽  
H. Guenther ◽  
M. Hartung
Keyword(s):  
Nmr Studies ◽  
X Ray
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